Obama signed off on arming the rebels in the spring of 2013, it was partly to try to gain control of the apparent free-for-all in the region. The Qataris and the Saudis had already been funneling weapons into Syria for more than a year.

President Barack Obama shakes hands with Saudi Arabia’s Crown Prince Mohammed bin Nayef during their meeting in the Oval Office of the White House in Washington, Wednesday, May 13, 2015. (AP Photo/Jacquelyn Martin)

WASHINGTON — When President Obama secretly authorized the Central Intelligence Agency to begin arming Syria’s embattled rebels in 2013, the spy agency knew it would have a willing partner to help pay for the covert operation. It was the same partner the C.I.A. has relied on for decades for money and discretion in far-off conflicts: the Kingdom of Saudi Arabia.

Since then, the C.I.A. and its Saudi counterpart have maintained an unusual arrangement for the rebel-training mission, which the Americans have code-named Timber Sycamore. Under the deal, current and former administration officials said, the Saudis contribute both weapons and large sums of money, and the C.I.A takes the lead in training the rebels on AK-47 assault rifles and tank-destroying missiles.

The support for the Syrian rebels is only the latest chapter in the decadeslong relationship between the spy services of Saudi Arabia and the United States, an alliance that has endured through the Iran-contra scandal, support for the mujahedeen against the Soviets in Afghanistan and proxy fights in Africa. Sometimes, as in Syria, the two countries have worked in concert. In others, Saudi Arabia has simply written checks underwriting American covert activities.

The joint arming and training program, which other Middle East nations contribute money to, continues as America’s relations with Saudi Arabia — and the kingdom’s place in the region — are in flux. The old ties of cheap oil and geopolitics that have long bound the countries together have loosened as America’s dependence on foreign oil declines and the Obama administration tiptoes toward a diplomatic rapprochement with Iran.

And yet the alliance persists, kept afloat on a sea of Saudi money and a recognition of mutual self-interest. In addition to Saudi Arabia’s vast oil reserves and role as the spiritual anchor of the Sunni Muslim world, the long intelligence relationship helps explain why the United States has been reluctant to openly criticize Saudi Arabia for its human rights abuses, its treatment of women and its support for the extreme strain of Islam, Wahhabism, that has inspired many of the very terrorist groups the United States is fighting. The Obama administration did not publicly condemn Saudi Arabia’s beheading this month of a dissident Shiite cleric, Sheikh Nimr al-Nimr, who had challenged the royal family.

Although the Saudis have been public about their help arming rebel groups in Syria, the extent of their partnership with the C.I.A.’s covert action campaign and their direct financial support had not been disclosed. Details were pieced together in interviews with a half-dozen current and former American officials and sources from several Persian Gulf countries. Most spoke on the condition of anonymity because they were not authorized to discuss the program.

From the moment the C.I.A. operation was started, Saudi money supported it.

“They understand that they have to have us, and we understand that we have to have them,” said Mike Rogers, the former Republican congressman from Michigan who was chairman of the House Intelligence Committee when the C.I.A. operation began. Mr. Rogers declined to discuss details of the classified program.

American officials have not disclosed the amount of the Saudi contribution, which is by far the largest from another nation to the program to arm the rebels against President Bashar al-Assad’s military. But estimates have put the total cost of the arming and training effort at several billion dollars.

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